working of get.mimarkspackage and sra command

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index e8e9c2754677ee639fce944fbc533d3bd9eb98db..8c5c0faef60a480a189f98994afc250e4c36a8c6 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -150,6 +150,7 @@
 #include "kruskalwalliscommand.h"
 #include "sracommand.h"
 #include "mergesfffilecommand.h"
+#include "getmimarkspackagecommand.h"
 
 /*******************************************************/
 
@@ -323,6 +324,7 @@ CommandFactory::CommandFactory(){
     commands["kruskal.wallis"]      = "kruskal.wallis";
     commands["sra"]                 = "sra";
     commands["merge.sfffiles"]      = "merge.sfffiles";
+    commands["get.mimarkspackage"]  = "get.mimarkspackage";
     
 
 }
@@ -552,6 +554,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
         else if(commandName == "kruskal.wallis")        {      command = new KruskalWallisCommand(optionString);           }
         else if(commandName == "sra")                   {      command = new SRACommand(optionString);                     }
         else if(commandName == "merge.sfffiles")        {      command = new MergeSfffilesCommand(optionString);           }
+        else if(commandName == "get.mimarkspackage")    {      command = new GetMIMarksPackageCommand(optionString);       }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -722,6 +725,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
         else if(commandName == "kruskal.wallis")        {      pipecommand = new KruskalWallisCommand(optionString);           }
         else if(commandName == "sra")                   {      pipecommand = new SRACommand(optionString);                     }
         else if(commandName == "merge.sfffiles")        {      pipecommand = new MergeSfffilesCommand(optionString);           }
+        else if(commandName == "get.mimarkspackage")    {      pipecommand = new GetMIMarksPackageCommand(optionString);       }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -878,6 +882,7 @@ Command* CommandFactory::getCommand(string commandName){
         else if(commandName == "kruskal.wallis")        {      shellcommand = new KruskalWallisCommand();          }
         else if(commandName == "sra")                   {      shellcommand = new SRACommand();                    }
         else if(commandName == "merge.sfffiles")        {      shellcommand = new MergeSfffilesCommand();          }
+        else if(commandName == "get.mimarkspackage")    {      shellcommand = new GetMIMarksPackageCommand();      }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;